Why Do I Feel Sick Taking Probiotics? Understanding the Causes and Cures

October 16, 2025 •

4 min read

According to a 2012 survey, probiotic use among U.S. adults had quadrupled since 2007. Despite their widespread use, some people find themselves asking, "Why do I feel sick taking probiotics?" This initial discomfort is a sign that your body's gut microbiome is undergoing a significant adjustment.

Quick Summary

Experiencing mild digestive upset like nausea, gas, and bloating is a common, temporary side effect when first taking probiotics. The gut is simply adjusting to new bacteria, but persistent symptoms can point to deeper issues like SIBO or histamine intolerance.

Key Points

Initial adjustment is normal: Mild digestive symptoms like gas, bloating, and nausea often occur as your gut microbiome adapts and are usually temporary, resolving within a few weeks.
SIBO can be a factor: Persistent or worsening symptoms may be a sign of underlying Small Intestinal Bacterial Overgrowth, where new bacteria can cause an adverse reaction.
Histamine sensitivity matters: Some probiotic strains produce histamine, which can cause headaches or allergy-like symptoms in sensitive individuals.
Start low and go slow: To minimize side effects, begin with a lower dose and gradually increase it over time to allow your body to adjust.
Choose quality products: As the industry is not heavily regulated, selecting a product from a reputable company with specific, well-researched strains is crucial for safety and efficacy.
Seek medical advice for severe symptoms: If discomfort persists or is severe, consult a healthcare provider to explore potential underlying causes and get personalized advice.

The Gut's Big Adjustment: Why You Might Feel Ill

When you introduce new probiotic bacteria into your digestive tract, your existing gut microbiome needs to adjust. This can lead to a period of digestive discomfort that, while unpleasant, is usually temporary. The new beneficial bacteria compete for space and resources with the existing microorganisms, causing a temporary imbalance that can manifest as various symptoms. This is often referred to as the Herxheimer reaction or a "die-off" effect, where the death of harmful bacteria releases toxins, triggering short-term discomfort.

Common Side Effects During the Initial Phase

For most people, the negative sensations subside within a few days or weeks as the gut rebalances. Here are some of the most common, temporary side effects:

Gas and bloating: New bacteria may produce more gas as a byproduct of fermenting prebiotics or other food in your gut. This is a common and normal part of the adjustment.
Nausea: A temporary feeling of nausea can occur as your stomach acid production shifts and your gut flora adjusts. Taking probiotics with food can often alleviate this.
Changes in bowel movements: You might experience softer stools, temporary diarrhea, or even short-term constipation. These changes are a result of your digestive system adapting to the new bacterial population.
Headaches: The breakdown of proteins by gut bacteria can produce biogenic amines like histamine, which some individuals are sensitive to and can trigger headaches.
Skin irritations: In rare cases, rashes or itchiness can occur as your body eliminates toxins released during the die-off period. This often resolves as the microbiome stabilizes.

When Symptoms Signal a Deeper Issue

While temporary discomfort is normal, persistent or severe symptoms may indicate an underlying condition. It is important to pay attention to your body's signals and consult a healthcare provider if problems do not resolve.

Small Intestinal Bacterial Overgrowth (SIBO)

Small Intestinal Bacterial Overgrowth (SIBO) is a condition where an excessive amount of bacteria, including beneficial ones, inhabit the small intestine. Introducing more bacteria via probiotics can exacerbate symptoms like bloating, gas, abdominal pain, and even brain fog in individuals with undiagnosed SIBO. For these people, taking probiotics may make them feel worse rather than better.

Histamine Intolerance

Some probiotic strains, particularly Lactobacillus casei and Lactobacillus bulgaricus, are known to produce histamine. If you have histamine intolerance, consuming these probiotics can cause allergy-like symptoms such as headaches, flushing, itching, or digestive issues. It is crucial to choose low-histamine strains or consult a specialist if you suspect this may be the cause.

Weakened Immune System

Individuals who are critically ill, have a compromised immune system, or are recovering from major surgery face a higher risk of adverse effects from probiotics, including infections. The live bacteria can potentially cause severe infections like sepsis in these vulnerable populations, though this is rare. It is essential for these individuals to seek medical advice before starting any probiotic regimen.

Product Quality and Ingredients

The effectiveness and safety of probiotic supplements are not regulated by the FDA in the same way as medications. Therefore, product quality can vary significantly. Issues may arise from ingredients other than the bacteria, such as fillers or prebiotics, which can also cause digestive upset. Ensure you choose a high-quality product from a reputable manufacturer that lists specific strains and guarantees potency.

How to Mitigate and Manage Probiotic Side Effects

There are several strategies to help your body adapt more smoothly to probiotics and minimize discomfort:

Start with a lower dose: Begin with a smaller number of colony-forming units (CFUs) and gradually increase the dosage over time. This allows your gut to adjust more gently.
Take with food: Taking your probiotic with a meal can help protect the bacteria from stomach acid and may reduce feelings of nausea. For some strains, taking them on an empty stomach is recommended, so check the product instructions.
Stay hydrated: Drinking plenty of water supports the mucosal lining of the gut and helps flush out toxins, potentially easing side effects.
Temporarily stop use: If symptoms are severe or persistent, pause your probiotic use. You can re-introduce it at a lower dose after your symptoms have resolved.
Adjust your diet: Reducing sugary and inflammatory foods can help, as these can feed harmful bacteria. Incorporating prebiotic foods, like garlic and onions, can also support the new bacteria.


Probiotic Strain/Type	Common Uses	Potential Side Effects	Notes
Lactobacillus acidophilus	Digestion, lactose intolerance	Gas, bloating, nausea	Many people adapt quickly; often found in yogurt
Bifidobacterium longum	IBS symptoms, gut wall integrity	Gas, bloating, digestive discomfort	A common resident of the adult gut
Saccharomyces boulardii	Combating antibiotic-associated diarrhea	Increased thirst, gas	A yeast-based probiotic; check for yeast allergies
Lactobacillus casei	Digestion, immune support	Potential histamine production	Can trigger issues for those with histamine intolerance

Conclusion: Most Discomfort is Temporary

While the initial experience of feeling sick from probiotics can be unsettling, it is often a normal, temporary sign of your gut microbiome adapting to the new beneficial bacteria. By understanding the common side effects and implementing strategies like starting with a low dose and taking with food, most people can manage this transition smoothly. However, if symptoms are severe, persistent, or accompanied by other concerning signs, it is crucial to consult a healthcare professional to rule out underlying issues like SIBO or other sensitivities. With proper care and guidance, probiotics can still be a powerful tool for supporting overall digestive health.

For more detailed information on probiotic safety and efficacy, you can consult resources from the National Center for Complementary and Integrative Health (NCCIH).

Frequently Asked Questions

Yes, it is common to experience mild and temporary side effects, such as gas, bloating, and nausea, when you first begin a probiotic regimen. This is typically a sign of your gut microbiome adjusting to the new bacteria.

For most healthy individuals, mild digestive side effects usually subside within a few days to a few weeks. If your discomfort persists beyond this period, it is recommended to speak with a doctor.

Yes, some people experience headaches from probiotics. This can be due to the production of biogenic amines like histamine by certain bacterial strains, which can affect blood flow to the central nervous system.

To reduce nausea, try taking your probiotic with a meal, as food can help buffer the supplement's effects and protect the bacteria. You can also start with a smaller dose.

The Herxheimer reaction, or "die-off" effect, occurs when a large number of harmful bacteria are killed off by probiotics, releasing toxins that cause temporary symptoms like gas, bloating, and fatigue.

For mild, temporary symptoms, you can try adjusting the dose or timing. However, if symptoms are severe, persistent, or you have a compromised immune system, you should stop taking them and consult a doctor.

Yes, if you have Small Intestinal Bacterial Overgrowth (SIBO), introducing additional bacteria through probiotics can potentially worsen symptoms like bloating and gas. A diagnosis from a healthcare professional is necessary to determine the right course of action.